stdout fix

sequencing · Feb 28, 2016 · 3891d10 · 3891d10
1 parent cdbe798
commit 3891d10
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Showing 4 changed files with 48 additions and 39 deletions.
diff --git a/fastqlib.cpp b/fastqlib.cpp
@@ -167,25 +167,36 @@ fastqWriter::fastqWriter(string fname){
 }
 
 int fastqWriter::open(string fname){
-  fp = gzopen(fname.c_str(), "wb");
-  if(!fp ) {
-    cerr << "Problem reading "<<fname<<endl;
-    exit(1);
+  if(fname=="-") {//STDOUT
+    _stdout=true;
+  }
+  else{
+    _stdout=false;
+    fp = gzopen(fname.c_str(), "wb");
+    if(!fp ) {
+      cerr << "Problem reading "<<fname<<endl;
+      exit(1);
+    }
   }
   return(0);
 }
 
 int fastqWriter::write(fqread & read) {
   if(read.l>0) {
-    if(gzwrite(fp,"@",1)==0) die("problem writing output");
-    if(gzwrite(fp,(char *)read.h.c_str(),read.h.size())==0) die("problem writing output");
-    if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
-    if( gzwrite(fp,(char *)read.s.c_str(),read.s.size())==0) die("problem writing output");
-    if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
-    if(    gzwrite(fp,(char *)read.l3.c_str(),read.l3.size())==0) die("problem writing output");
-    if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
-    if(    gzwrite(fp,(char *)read.q.c_str(),read.q.size())==0) die("problem writing output");
-    if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
+    if(_stdout) {
+      read.print();
+    }
+    else{
+      if(gzwrite(fp,"@",1)==0) die("problem writing output");
+      if(gzwrite(fp,(char *)read.h.c_str(),read.h.size())==0) die("problem writing output");
+      if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
+      if( gzwrite(fp,(char *)read.s.c_str(),read.s.size())==0) die("problem writing output");
+      if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
+      if(    gzwrite(fp,(char *)read.l3.c_str(),read.l3.size())==0) die("problem writing output");
+      if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
+      if(    gzwrite(fp,(char *)read.q.c_str(),read.q.size())==0) die("problem writing output");
+      if(    gzwrite(fp,"\n",1)==0) die("problem writing output");
+    }
     return(1);
   }
   else  return(0);

diff --git a/fastqlib.h b/fastqlib.h
@@ -59,6 +59,7 @@ class fastqWriter {
   int write(readPair & read);
  private:
   gzFile fp;
+  bool _stdout;//true if writing to stdout
 };
 
 class pairReader {
@@ -78,7 +79,7 @@ class pairWriter {
 
   //interleaved
   pairWriter(string fname);
-  int  open(string fname);
+  int open(string fname);
   //separate files
   pairWriter(string fname1,string fname2);
   int  open(string fname1,string fname2);

diff --git a/matepair.cpp b/matepair.cpp
@@ -516,24 +516,29 @@ nxtrimWriter::nxtrimWriter(string prefix,bool jmp,bool separate) {
 }
 
 int nxtrimWriter::open(string prefix,bool jmp,bool separate) {
+  if(prefix=="-")
+    return(open(jmp,separate));
   n_mp=0;
   n_pe=0;
   n_se=0;
   n_unk=0;
   justmp = jmp;
 
-  if(separate)     mp_out.open(prefix+"_R1.mp.fastq.gz", prefix+"_R2.mp.fastq.gz");
-  else     mp_out.open(prefix+".mp.fastq.gz");
+  if(separate)     
+    mp_out.open(prefix+"_R1.mp.fastq.gz", prefix+"_R2.mp.fastq.gz");
+  else     
+    mp_out.open(prefix+".mp.fastq.gz");
 
-  if(separate)    unknown_out.open(prefix+"_R1.unknown.fastq.gz",prefix+"_R2.unknown.fastq.gz");
-  else unknown_out.open(prefix+".unknown.fastq.gz");  
+  if(separate)    
+    unknown_out.open(prefix+"_R1.unknown.fastq.gz",prefix+"_R2.unknown.fastq.gz");
+  else 
+    unknown_out.open(prefix+".unknown.fastq.gz");  
 
   if(!justmp) {
     if(separate) pe_out.open(prefix+"_R1.pe.fastq.gz",prefix+"_R2.pe.fastq.gz");
     else  pe_out.open(prefix+".pe.fastq.gz");
     se_out.open(prefix+".se.fastq.gz");
   }
-  print_to_stdout=false;
   return(0);
 }
 
@@ -549,29 +554,21 @@ int nxtrimWriter::open(bool jmp,bool separate) {
   n_se=0;
   n_unk=0;
   justmp = jmp;
-
-  print_to_stdout=true;
+  mp_out.open("-");
+  pe_out.open("-");
+  unknown_out.open("-");
+  se_out.open("-");
   return(0);
 }
 
 int nxtrimWriter::write(matePair m) {
-  if(!print_to_stdout) {
-    n_mp+=mp_out.write(m.mp);
-    n_unk+=unknown_out.write(m.unknown);  
-    if(!justmp) {
-      n_pe+=pe_out.write(m.pe);
-      n_se+=se_out.write(m.se);  
-    }
-    if(DEBUG>0)
-      cerr << "Wrote: n_mp="<<n_mp<<" n_unk="<<n_unk<<" n_pe="<<n_pe<<" n_se="<<n_se<<endl;
-  }
-  else{    
-    m.mp.print();
-    m.unknown.print();
-    if(!justmp) {
-      m.pe.print();
-      m.se.print();  
-    }
+  n_mp+=mp_out.write(m.mp);
+  n_unk+=unknown_out.write(m.unknown);  
+  if(!justmp) {
+    n_pe+=pe_out.write(m.pe);
+    n_se+=se_out.write(m.se);  
   }
+  if(DEBUG>0)      cerr << "Wrote: n_mp="<<n_mp<<" n_unk="<<n_unk<<" n_pe="<<n_pe<<" n_se="<<n_se<<endl;
+
   return(0);
 }
diff --git a/nxtrim.cpp b/nxtrim.cpp
@@ -139,7 +139,7 @@ int main(int argc,char **argv) {
 
   nxtrimWriter out;
   if(write_stdout) 
-    out.open(justmp,separate);
+    out.open("-",justmp,separate);
   else  
     out.open(prefix,justmp,separate);